Been A while since you posted this, any news?
Just to clarify I know nothing about Audis but apparently the 140ps version was knows for a few faults,
The only think i could think of with a Diesel engine misfiring, is either the Timing is off/Fuel Air ratio off or Dirty fuel producing a incomplete bang
Could try some Diesel Redex perhaps?
Thats it Im afraid, hopefully someone mechanically minded will be along soon